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Kaltman JR, Evans F, Fu YP. Re-evaluating pathogenicity of variants associated with the long QT syndrome. J Cardiovasc Electrophysiol 2017; 29:98-104. [PMID: 28988457 DOI: 10.1111/jce.13355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/17/2017] [Accepted: 09/11/2017] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Genetic testing for congenital long QT syndrome (LQTS) has become common. Recent studies have shown that some variants labelled as pathogenic might be misclassified due to sparse case reports and relatively common allele frequencies (AF) in the general population. This study aims to evaluate the presence of LQTS-associated variants in the Genome Aggregation Database (gnomAD) population, and assess the functional impact of these variants. METHODS AND RESULTS Variants associated with LQTS from the Human Gene Mutation Database were extracted and matched to the gnomAD to evaluate population-based AF. We used MetaSVM to predict the function of LQTS variants. Allele distribution by protein topology in KCNQ1, KCNH2, and SCN5A was compared between gnomAD (n = 123,136) and a cohort of LQTS patients aggregated from eight published studies (n = 2,683). Among the 1,415 LQTS-associated single nucleotide variants in 30 genes, 347 (25%) are present in gnomAD; 24% of the 347 variants were predicted as functionally tolerated compared with 4% of variants not present in gnomAD (P < 0.001). Of the 347 pathogenic variants in gnomAD, seven (2%) had an AF of ≥ 0.001 and 65 (19%) variants had an AF of ≥ 0.0001. In KCNQ1, KCNH2, and SCN5A, allele distribution by protein functional region was significantly different with gnomAD alleles appearing less frequently in highly pathogenic domains than case alleles. CONCLUSION A significant number of LQTS variants have insufficient evidence for pathogenicity and relatively common AF in the general population. Caution should be used when ascribing pathogenicity to these variants.
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Affiliation(s)
- Jonathan R Kaltman
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Frank Evans
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Yi-Ping Fu
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
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Kong T, Feulefack J, Ruether K, Shen F, Zheng W, Chen XZ, Sergi C. Ethnic Differences in Genetic Ion Channelopathies Associated with Sudden Cardiac Death: A Systematic Review and Meta-Analysis. Ann Clin Lab Sci 2017; 47:481-490. [PMID: 28801377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND AIMS Reports of allele frequencies encoding ion channel, or their interacting proteins associated with sudden cardiac death among different ethnic groups have been inconsistent. Here, we aimed to characterize the distribution of these genes and their alleles among various ethnicities through meta-analysis. METHODS We conducted a systematic review and meta-analysis to assess the mean allele frequencies of channelopathy genes SCN5A, NOS1AP, KCNH2, KCNE1, and KCNQ1 among the Black, Caucasian, Asian, and Hispanic ethnicities. Searches in PubMed, Google Scholar, and Web of Science resulted in 18 reports published before July 2015 that met the eligible criteria. Allele frequencies were averaged by weight, and pooled values were calculated by inverse variance. Fixed-effects and random-effects models were used to pool effect sizes within each study and across different studies, respectively. Moreover, to extend our findings, we used sequenced genomic data from the Exome Aggregation Consortium to compare allele frequencies between different ethnicities. RESULTS Meta-analysis of published studies supports that Asians had the highest overall mean allele frequencies of NOS1AP (0.36%, 95% CI: 0.30, 0.43; P<0.001), and SCN5A frequencies (0.17%, 95% CI: 0.07, 0.27, P=0.001), and whereas Caucasians had the highest KCNH2 frequency (0.21%, 95% CI: 0.16, 0.25; P<0.001), and Hispanics the highest KCNQ1 frequency (0.16%). Analysis of the Exome Aggregation Consortium also provided consistent data in agreement the meta-analysis. CONCLUSION Overall, Asians carried the most alleles of genes associated with sudden cardiac death. The meta-analysis reveals significant differences in allele distribution of channelopathy-associated genes among different ethnic groups.
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Affiliation(s)
- Tim Kong
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
- Membrane Protein Disease Research Group, Department of Physiology, University of Alberta, Edmonton, Edmonton, Canada
- Department of Biochemistry, McGill University, Montréal, Quebec, Edmonton, Canada
| | - Joseph Feulefack
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Kim Ruether
- Diagnostic Imaging Fairview Health Complex, Fairview, Alberta, Edmonton, Canada
| | - Fan Shen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
- Membrane Protein Disease Research Group, Department of Physiology, University of Alberta, Edmonton, Edmonton, Canada
| | - Wang Zheng
- Membrane Protein Disease Research Group, Department of Physiology, University of Alberta, Edmonton, Edmonton, Canada
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, University of Alberta, Edmonton, Edmonton, Canada
| | - Consolato Sergi
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
- Stollery Children's Hospital, Department of Pediatrics, Univ. of Alberta, Edmonton, Canada
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Suri M, Evers JMG, Laskowski RA, O'Brien S, Baker K, Clayton-Smith J, Dabir T, Josifova D, Joss S, Kerr B, Kraus A, McEntagart M, Morton J, Smith A, Splitt M, Thornton JM, Wright CF. Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1. Mol Genet Genomic Med 2017; 5:495-507. [PMID: 28944233 PMCID: PMC5606886 DOI: 10.1002/mgg3.304] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/17/2017] [Accepted: 05/20/2017] [Indexed: 01/07/2023] Open
Abstract
Background Syntaxin‐binding protein 1, encoded by STXBP1, is highly expressed in the brain and involved in fusing synaptic vesicles with the plasma membrane. Studies have shown that pathogenic loss‐of‐function variants in this gene result in various types of epilepsies, mostly beginning early in life. We were interested to model pathogenic missense variants on the protein structure to investigate the mechanism of pathogenicity and genotype–phenotype correlations. Methods We report 11 patients with pathogenic de novo mutations in STXBP1 identified in the first 4293 trios of the Deciphering Developmental Disorder (DDD) study, including six missense variants. We analyzed the structural locations of the pathogenic missense variants from this study and the literature, as well as population missense variants extracted from Exome Aggregation Consortium (ExAC). Results Pathogenic variants are significantly more likely to occur at highly conserved locations than population variants, and be buried inside the protein domain. Pathogenic mutations are also more likely to destabilize the domain structure compared with population variants, increasing the proportion of (partially) unfolded domains that are prone to aggregation or degradation. We were unable to detect any genotype–phenotype correlation, but unlike previously reported cases, most of the DDD patients with STXBP1 pathogenic variants did not present with very early‐onset or severe epilepsy and encephalopathy, though all have developmental delay with intellectual disability and most display behavioral problems and suffered seizures in later childhood. Conclusion Variants across STXBP1 that cause loss of function can result in severe intellectual disability with or without seizures, consistent with a haploinsufficiency mechanism. Pathogenic missense mutations act through destabilization of the protein domain, making it prone to aggregation or degradation. The presence or absence of early seizures may reflect ascertainment bias in the literature as well as the broad recruitment strategy of the DDD study.
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Affiliation(s)
- Mohnish Suri
- Nottingham Regional Genetics ServiceNottingham University Hospitals NHS TrustCity Hospital Campus, The Gables, Hucknall RoadNottinghamNG5 1PBUK
| | - Jochem M G Evers
- European Bioinformatics Institute (EMBL-EBI)Wellcome Genome Campus, HinxtonCambridgeCB10 1SDUK
| | - Roman A Laskowski
- European Bioinformatics Institute (EMBL-EBI)Wellcome Genome Campus, HinxtonCambridgeCB10 1SDUK
| | - Sinead O'Brien
- MRC Cognition and Brain Sciences Unit15 Chaucer RoadCambridgeCB2 7EFUK
| | - Kate Baker
- MRC Cognition and Brain Sciences Unit15 Chaucer RoadCambridgeCB2 7EFUK.,Department of Medical GeneticsUniversity of CambridgeCambridge Biomedical CampusCambridgeCB2 0QQUK
| | - Jill Clayton-Smith
- Manchester Centre for Genomic MedicineSt Mary's Hospital, Central Manchester University Hospitals NHS Foundation TrustManchester Academic Health Science CentreManchesterM13 9WLUK
| | - Tabib Dabir
- Northern Ireland Regional Genetics CentreBelfast Health and Social Care TrustBelfast City HospitalLisburn RoadBelfastBT9 7ABUK
| | - Dragana Josifova
- South East Thames Regional Genetics CentreGuy's and St Thomas' NHS Foundation TrustGuy's HospitalGreat Maze PondLondonSE1 9RTUK
| | - Shelagh Joss
- West of Scotland Genetics ServiceQueen Elizabeth University HospitalLaboratory Medicine BuildingGlasgowG51 4TFUK
| | - Bronwyn Kerr
- Manchester Centre for Genomic MedicineSt Mary's Hospital, Central Manchester University Hospitals NHS Foundation TrustManchester Academic Health Science CentreManchesterM13 9WLUK
| | - Alison Kraus
- Yorkshire Regional Genetics ServiceDepartment of Clinical GeneticsLeeds Teaching Hospitals NHS TrustChapel Allerton HospitalChapeltown RoadLeedsLS7 4SAUK
| | - Meriel McEntagart
- South West Thames Regional Genetics CentreSt George's Healthcare NHS TrustSt George's University of LondonCranmer TerraceLondonSW17 0REUK
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health PartnersBirmingham Women's and Children's NHS Foundation TrustBirmingham Women's HospitalMindelsohn Way, EdgbastonBirminghamB15 2TGUK
| | - Audrey Smith
- Yorkshire Regional Genetics ServiceDepartment of Clinical GeneticsLeeds Teaching Hospitals NHS TrustChapel Allerton HospitalChapeltown RoadLeedsLS7 4SAUK
| | - Miranda Splitt
- Northern Genetics ServiceNewcastle upon Tyne Hospitals NHS Foundation TrustInstitute of Human GeneticsInternational Centre for LifeCentral ParkwayNewcastle upon TyneNE1 3BZUK
| | - Janet M Thornton
- European Bioinformatics Institute (EMBL-EBI)Wellcome Genome Campus, HinxtonCambridgeCB10 1SDUK
| | | | - Caroline F Wright
- Wellcome Trust Sanger InstituteWellcome Genome Campus, HinxtonCambridgeCB1 8RQUK.,University of Exeter Medical SchoolRoyal Devon & Exeter HospitalBarrack RoadExeterEX2 5DWUK
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Carlston CM, O'Donnell-Luria AH, Underhill HR, Cummings BB, Weisburd B, Minikel EV, Birnbaum DP, Tvrdik T, MacArthur DG, Mao R. Pathogenic ASXL1 somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome. Hum Mutat 2017; 38:517-523. [PMID: 28229513 DOI: 10.1002/humu.23203] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/31/2017] [Accepted: 02/18/2017] [Indexed: 01/09/2023]
Abstract
The clinical interpretation of genetic variants has come to rely heavily on reference population databases such as the Exome Aggregation Consortium (ExAC) database. Pathogenic variants in genes associated with severe, pediatric-onset, highly penetrant, autosomal dominant conditions are assumed to be absent or rare in these databases. Exome sequencing of a 6-year-old female patient with seizures, developmental delay, dysmorphic features, and failure to thrive identified an ASXL1 variant previously reported as causative of Bohring-Opitz syndrome (BOS). Surprisingly, the variant was observed seven times in the ExAC database, presumably in individuals without BOS. Although the BOS phenotype fit, the presence of the variant in reference population databases introduced ambiguity in result interpretation. Review of the literature revealed that acquired somatic mosaicism of ASXL1 variants (including pathogenic variants) during hematopoietic clonal expansion can occur with aging in healthy individuals. We examined all ASXL1 truncating variants in the ExAC database and determined most are likely somatic. Failure to consider somatic mosaicism may lead to the inaccurate assumption that conditions like BOS have reduced penetrance, or the misclassification of potentially pathogenic variants.
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Affiliation(s)
- Colleen M Carlston
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Hunter R Underhill
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah.,Department of Radiology, University of Utah, Salt Lake City, Utah
| | - Beryl B Cummings
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Ben Weisburd
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Eric V Minikel
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Daniel P Birnbaum
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | | | - Tatiana Tvrdik
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Rong Mao
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
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